Minor histocompatibility antigens (mHA) are peptides derived from normal cellular proteins presented by major histocompatibility complex (MHC) class I and class II molecules. Following allogeneic hematopoietic stem cell transplantation (HSCT), recipient mHA are recognized by donor T cells and become the primary targets of graft-vs-host disease (GVHD). To the extent that mHA are expressed on leukemia cells, these antigens also become important targets of graft-vs-leukemia (GVL) following HSCT. Several well-defined mHA are encoded by genes on the Y chromosome, and CD4+ and CD8+ T cell responses to HY antigens following allogeneic HSCT can mediate GVHD and GVL. Using HY proteins as a model for human mHA, previous laboratory studies in this project demonstrated that male patients engrafted with stem cells from female donors frequently develop antibodies that recognize Y-encoded proteins after transplant. HY antibodies typically develop 4-8 months after transplant and do not occur in patients who receive stem cells from gender-matched donors. HY antibodies persist at high titer for prolonged periods and are significantly associated with the development of chronic GVHD. In studies described in Project 1, these observations led to the evaluation of B cell directed therapy with rituximab for patients with steroid resistant chronic GVHD with promising clinical results. Although these observations suggest that antibodies specific for mHA play a role in chronic GVHD, the mechanisms whereby HY antibodies contribute to tissue damage in affected organs have not been elucidated. To better define the role of B cells and antibodies in the pathogenesis of chronic GVHD, proposed studies in Project 3 will develop new genomic and proteomic approaches to define the spectrum of antibody targets in patients with chronic GVHD and to identify clinically relevant new mHA. Proposed studies will also examine B Cell Activating Factor (BAFF) as a potential biologically relevant marker of chronic GVHD and define the mechanisms whereby B cells and antibodies interact with T cells and contribute to GVHD and GVL following HSCT. There are 4 Specific Aims in Project 3. 1 .Define the spectrum of B cell target antigens in patients with chronic GVHD. 2. Identify novel mHA through genomic comparisons of HLA-identical recipients and donors. 3. Determine whether soluble BAFF levels accurately predict the development of chronic GVHD. 4. Define the mechanisms whereby B cells and antibodies contribute to the development of tissue damage following allogeneic HSCT.